enrichMKEGG can not identify the species
1
@bright602-14940
Last seen 6.3 years ago
Hi there,
Recently I tried to use enrichMKEGG or enrichKEGG function from clusterProfiler, however, there is an error message stating that
Error in download.KEGG.Module(species) : 'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html' ...
Even I tried to to use the example from vignette, and still have the same problem.
library(clusterProfiler)
Could anyone give me some suggestions?
Thanks,
Sim
clusterprofiler
• 4.9k views
@guido-hooiveld-2020
Last seen 23 minutes ago
Wageningen University, Wageningen, the …
You did not define the object de, which you used as input. Also, the last line of your code is weird; why do you include head(summary(xx))?
Example from vignette is running fine for me (please note my comments):
> library(clusterProfiler)
> data(geneList, package='DOSE')
> de <- names(geneList)[1:100]
>
> # run function enrichKEGG (for KEGG categories)
>
> yy <- enrichKEGG(de, organism='hsa', pvalueCutoff=0.01)
> head(yy)
ID Description GeneRatio BgRatio pvalue
hsa04110 hsa04110 Cell cycle 8/46 124/7431 7.353075e-07
hsa04218 hsa04218 Cellular senescence 7/46 160/7431 4.970308e-05
hsa04114 hsa04114 Oocyte meiosis 6/46 124/7431 1.037461e-04
hsa04657 hsa04657 IL-17 signaling pathway 5/46 93/7431 2.518699e-04
hsa04914 hsa04914 Progesterone-mediated oocyte maturation 5/46 99/7431 3.371863e-04
p.adjust qvalue geneID Count
hsa04110 8.088382e-05 7.662678e-05 8318/991/9133/890/983/4085/7272/1111 8
hsa04218 2.733669e-03 2.589792e-03 2305/4605/9133/890/983/51806/1111 7
hsa04114 3.804024e-03 3.603812e-03 991/9133/983/4085/51806/6790 6
hsa04657 6.926423e-03 6.561874e-03 4312/6280/6279/6278/3627 5
hsa04914 7.418099e-03 7.027673e-03 9133/890/983/4085/6790 5
>
>
> # run function enrichMKEGG (for KEGG modules)
> # note p-value cutoff has been increased to
> # p=0.1, because otherwise no modules pass cutoff.
>
> zz <- enrichMKEGG(de, organism='hsa', pvalueCutoff=0.1)
> head(zz)
ID Description GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
M00389 M00389 APC/C complex 1/7 14/1522 0.06275953 0.06275953 NA 991 1
>
> sessionInfo()
R version 3.5.1 Patched (2018-07-12 r74967)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] clusterProfiler_3.8.1 BiocInstaller_1.30.0
loaded via a namespace (and not attached):
[1] ggrepel_0.8.0 Rcpp_0.12.17 lattice_0.20-35 tidyr_0.8.1
[5] GO.db_3.6.0 assertthat_0.2.0 digest_0.6.15 ggforce_0.1.3
[9] R6_2.2.2 plyr_1.8.4 ggridges_0.5.0 stats4_3.5.1
[13] RSQLite_2.1.1 ggplot2_3.0.0 pillar_1.3.0 rlang_0.2.1
[17] lazyeval_0.2.1 data.table_1.11.4 blob_1.1.1 S4Vectors_0.18.3
[21] Matrix_1.2-14 qvalue_2.12.0 splines_3.5.1 BiocParallel_1.14.2
[25] stringr_1.3.1 igraph_1.2.1 bit_1.1-14 munsell_0.5.0
[29] fgsea_1.6.0 compiler_3.5.1 pkgconfig_2.0.1 BiocGenerics_0.26.0
[33] tidyselect_0.2.4 tibble_1.4.2 gridExtra_2.3 IRanges_2.14.10
[37] enrichplot_1.0.2 viridisLite_0.3.0 crayon_1.3.4 dplyr_0.7.6
[41] MASS_7.3-50 grid_3.5.1 gtable_0.2.0 DBI_1.0.0
[45] magrittr_1.5 units_0.6-0 scales_0.5.0 stringi_1.2.3
[49] GOSemSim_2.6.0 reshape2_1.4.3 viridis_0.5.1 bindrcpp_0.2.2
[53] DO.db_2.9 rvcheck_0.1.0 cowplot_0.9.3 fastmatch_1.1-0
[57] tools_3.5.1 bit64_0.9-7 Biobase_2.40.0 glue_1.3.0
[61] tweenr_0.1.5 purrr_0.2.5 ggraph_1.0.2 parallel_3.5.1
[65] AnnotationDbi_1.42.1 colorspace_1.3-2 UpSetR_1.3.3 DOSE_3.6.1
[69] memoise_1.1.0 bindr_0.1.1
>
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Thanks Guido, I tried to repeat but the same error message still pop out.
> library(clusterProfiler)
> data(geneList, package='DOSE')
> de <- names(geneList)[1:100]
> yy <- enrichKEGG(de, organism='hsa', pvalueCutoff=0.01)
Error in download.KEGG.Path(species) :
'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'...
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] org.Hs.eg.db_3.6.0 GSEABase_1.43.0 annotate_1.59.0
[4] XML_3.98-1.12 GO.db_3.6.0 DOSE_3.7.1
[7] BiocManager_1.30.1 RDAVIDWebService_1.19.0 GOstats_2.47.0
[10] Category_2.47.0 Matrix_1.2-14 AnnotationDbi_1.43.1
[13] IRanges_2.15.14 S4Vectors_0.19.17 Biobase_2.41.1
[16] graph_1.59.0 BiocGenerics_0.27.1 clusterProfiler_3.9.1
[19] ggplot2_3.0.0 ChIPseeker_1.17.0
Mmm, looks like you have a mix of release and development packages.... For R-3.5.x / Bioc-3.7 you should use
clusterProfilerversion 3.8.1 (here) (2nd number = an even number) , you have version 3.9.1 (2nd number = an odd number, thus the 'development' version). Maybe this explains your error; again, your code is running fine for me.... Please note that you have multiple dev packages installedThanks for reply. I will look into that and have a try.